fp <-here('vast','output','opilio_gadus_numbers')
setwd(fp)

Model options

load(paste0(fp,"/Record.RData"))
list2env(Record,envir = environment())
## <environment: R_GlobalEnv>
Record
## $Version
## [1] "VAST_v8_0_0"
## 
## $Method
## [1] "Mesh"
## 
## $n_x
## [1] 50
## 
## $Aniso
## [1] 1
## 
## $FieldConfig
##   Omega1 Epsilon1   Omega2 Epsilon2 
##        5        5        5        5 
## 
## $RhoConfig
##    Beta1    Beta2 Epsilon1 Epsilon2 
##        0        0        0        0 
## 
## $OverdispersionConfig
## Eta1 Eta2 
##    0    0 
## 
## $VamConfig
## Method   Rank Timing 
##      0      0      0 
## 
## $ObsModel
## [1] 1 0
## 
## $Region
## [1] "Eastern_Bering_Sea"
## 
## $Species_set
## [1] "Opilio immature" "Opilio spawner"  "small cod"       "medium cod"     
## [5] "large cod"      
## 
## $strata.limits
##      STRATA
## 1 All_areas
## 
## $Options
##          SD_site_density       SD_site_logdensity          Calculate_Range 
##                        0                        0                        1 
##       Calculate_evenness Calculate_effective_area         Calculate_Cov_SE 
##                        0                        1                        0 
##      Calculate_Synchrony      Calculate_Coherence 
##                        0                        0

Model diagnostics

Residuals

Catch rate

knitr::include_graphics(paste0(fp,"/maps--catchrate_pearson_resid.png"))

Encounter rate

knitr::include_graphics(paste0(fp,"/Diag--Encounter_prob.png"))

knitr::include_graphics(paste0(fp,"/maps--encounter_pearson_resid.png"))

Direction of geometric anisotropy

knitr::include_graphics(paste0(fp,"/Aniso.png"))

Q-Q plots

# Opilio immature
knitr::include_graphics(paste0(fp,"/QQ_Fn/Posterior_Predictive-Histogram-1.jpg"))

# Spawners
knitr::include_graphics(paste0(fp,"/QQ_Fn/Posterior_Predictive-Histogram-2.jpg"))

# Small cod
knitr::include_graphics(paste0(fp,"/QQ_Fn/Posterior_Predictive-Histogram-3.jpg"))

# Medium cod
knitr::include_graphics(paste0(fp,"/QQ_Fn/Posterior_Predictive-Histogram-4.jpg"))

# Large cod
knitr::include_graphics(paste0(fp,"/QQ_Fn/Posterior_Predictive-Histogram-5.jpg"))

Model outputs

Covariance

Columnns: Omega, Epsilon (Spatial, Temporal variation, respectively)

Rows: Encounter probability, Positive catch rate

knitr::include_graphics(paste0(fp,"/Cov--Analytic.png"))

Biomass Index, Center of Gravity and Effective Area Occupied

knitr::include_graphics(paste0(fp,"/Index-Biomass.png"))

knitr::include_graphics(paste0(fp,"/center_of_gravity.png"))

knitr::include_graphics(paste0(fp,"/Effective_Area.png"))

Predicted Density (Log scale)

knitr::include_graphics(paste0(fp,"/dens_Opilio Immature.png"))

knitr::include_graphics(paste0(fp,"/dens_Opilio Spawner.png"))

knitr::include_graphics(paste0(fp,"/dens_Small Cod.png"))

knitr::include_graphics(paste0(fp,"/dens_Medium Cod.png"))

knitr::include_graphics(paste0(fp,"/dens_Large Cod.png"))

Correlation in Predicted Densities

knitr::include_graphics(paste0(fp,"/spp_correlations.png"))

Factor Loadings

knitr::include_graphics(paste0(fp,"/factor_loadings_rotated.png"))

Factor Maps (Spatial Average)

# Omega 1 (encounter probability, spatial variation)
knitr::include_graphics(paste0(fp,"/Factor_maps--Omega1.png"))

# Omega 2 (positive catch rate, spatial variation)
knitr::include_graphics(paste0(fp,"/Factor_maps--Omega2.png"))

# Epsilon 1 (encounter probability, spatiotemporal variation)
knitr::include_graphics(paste0(fp,"/Factor_maps--Epsilon1.png"))

# Epsilon 2 (positive catch rate, spatiotemporal variation)
knitr::include_graphics(paste0(fp,"/Factor_maps--Epsilon2.png"))

Factor Maps (Spatio-Temporal Annual Variation)

# Factor 1, Positive Catch Rate
knitr::include_graphics(paste0(fp,"/Eps_Pos--Factor_1.png"))

# Factor 2, Positive Catch Rate
knitr::include_graphics(paste0(fp,"/Eps_Pos--Factor_2.png"))

# Factor 3, Positive Catch Rate
knitr::include_graphics(paste0(fp,"/Eps_Pos--Factor_3.png"))

# Factor 4, Positive Catch Rate
knitr::include_graphics(paste0(fp,"/Eps_Pos--Factor_4.png"))

# Factor 5, Positive Catch Rate
knitr::include_graphics(paste0(fp,"/Eps_Pos--Factor_5.png"))

# Factor 1, Presence Absence
knitr::include_graphics(paste0(fp,"/Eps_Pres--Factor_1.png"))

# Factor 2, Presence Absence
knitr::include_graphics(paste0(fp,"/Eps_Pres--Factor_2.png"))

# Factor 3, Presence Absence
knitr::include_graphics(paste0(fp,"/Eps_Pres--Factor_3.png"))

# Factor 4, Presence Absence
knitr::include_graphics(paste0(fp,"/Eps_Pres--Factor_4.png"))

# Factor 5, Presence Absence
knitr::include_graphics(paste0(fp,"/Eps_Pres--Factor_5.png"))